Role of transposable elements in heterochromatin and epigenetic control

Zachary Lippman, Anne-Valérie Gendrel, Michael Black, Matthew W. Vaughn, Neilay Dedhia, W. Richard McCombie, Kimberly Lavine, Vivek Mittal, Bruce May, Kristin D. Kasschau, James C. Carrington, Rebecca W. Doerge, Vincent Colot () and Rob Martienssen ()
Additional contact information
Zachary Lippman: Watson School of Biological Sciences and Cold Spring Harbor Laboratory
Anne-Valérie Gendrel: INRA/CNRS/UEVE
Michael Black: Purdue University
Matthew W. Vaughn: Watson School of Biological Sciences and Cold Spring Harbor Laboratory
Neilay Dedhia: Watson School of Biological Sciences and Cold Spring Harbor Laboratory
W. Richard McCombie: Watson School of Biological Sciences and Cold Spring Harbor Laboratory
Kimberly Lavine: Watson School of Biological Sciences and Cold Spring Harbor Laboratory
Vivek Mittal: Watson School of Biological Sciences and Cold Spring Harbor Laboratory
Bruce May: Watson School of Biological Sciences and Cold Spring Harbor Laboratory
Kristin D. Kasschau: Oregon State University
James C. Carrington: Oregon State University
Rebecca W. Doerge: Purdue University
Vincent Colot: INRA/CNRS/UEVE
Rob Martienssen: Watson School of Biological Sciences and Cold Spring Harbor Laboratory

Nature, 2004, vol. 430, issue 6998, 471-476

Abstract: Abstract Heterochromatin has been defined as deeply staining chromosomal material that remains condensed in interphase, whereas euchromatin undergoes de-condensation1. Heterochromatin is found near centromeres and telomeres, but interstitial sites of heterochromatin (knobs) are common in plant genomes and were first described in maize2. These regions are repetitive and late-replicating3. In Drosophila, heterochromatin influences gene expression, a heterochromatin phenomenon called position effect variegation4. Similarities between position effect variegation in Drosophila and gene silencing in maize mediated by “controlling elements” (that is, transposable elements) led in part to the proposal that heterochromatin is composed of transposable elements, and that such elements scattered throughout the genome might regulate development2. Using microarray analysis, we show that heterochromatin in Arabidopsis is determined by transposable elements and related tandem repeats, under the control of the chromatin remodelling ATPase DDM1 (Decrease in DNA Methylation 1). Small interfering RNAs (siRNAs) correspond to these sequences, suggesting a role in guiding DDM1. We also show that transposable elements can regulate genes epigenetically, but only when inserted within or very close to them. This probably accounts for the regulation by DDM1 and the DNA methyltransferase MET1 of the euchromatic, imprinted gene FWA, as its promoter is provided by transposable-element-derived tandem repeats that are associated with siRNAs.

Date: 2004
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DOI: 10.1038/nature02651

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